Accelerating wavepacket propagation with machine learning.

In this work, we discuss the use of a recently introduced machine learning (ML) technique known as Fourier neural operators (FNO) as an efficient alternative to the traditional solution of the time-dependent Schrödinger equation (TDSE). FNOs are ML models which are employed in the approximated solution of partial differential equations. For a wavepacket propagating in an anharmonic potential and for a tunneling system, we show that the FNO approach can accurately and faithfully model wavepacket propagation via the density. Additionally, we demonstrate that FNOs can be a suitable replacement for traditional TDSE solvers in cases where the results of the quantum dynamical simulation are required repeatedly such as in the case of parameter optimization problems (e.g., control). The speed-up from the FNO method allows for its combination with the Markov-chain Monte Carlo approach in applications that involve solving inverse problems such as optimal and coherent laser control of the outcome of dynamical processes.

Automatic Determination of the Non-Covalent Stable Conformations of the NO2-Pyrene Cluster in Full Dimensionality (81D) Using the vdW-TSSCDS Approach.

We present the detailed topographical characterisation (stationary points and minimum energy paths connecting them) of the full dimensional (81D) intermolecular potential energy surface associated with the non-covalent interactions between the NO2 radical and the pyrene (C16H10) molecule. The whole procedure is (quasi) fully automated. We have used our recent algorithm vdW-TSSCDS as implemented on the freely-available AutoMekin software package. To this end, a series of inexpensive classical trajectories using forces from a low-level (semi-empirical) theory are used to sample the configuration space of the system in the search for candidates to first order saddle points. These guess structures are determined by means of a graph-theory based algorithm using the concept of adjacency matrix. Low-level optimizations are followed by re-optimizations at a final high-level of theory (DFT and CCSD(T)-F12 in our case.). The resulting set of stationary points and paths connecting them constitutes the so-called reaction network. In the case of NO2-pyrene, this network exhibits four major basins which can be characterized by their point-group symmetry. A central one, of global C2 symmetry, comprises the global minimum (as well as all other permutationally related conformers) together with the corresponding C2v saddle points connecting them. This central basin is connected to three others of lower C1 symmetry. The latter can be distinguished by the projection of the position of the NO2 nitrogen atom on the pyrene plane in combination with the relative orientation of the oxygen pair pointing either inwards, outwards, upwards or downwards.

Apoptotic Marker Expression of Resected Lacrimal Gland Adenoid Cystic Carcinoma Tumor Margins After Intra-arterial Chemotherapy and Globe-Sparing Excision.

PURPOSE: Lacrimal gland adenoid cystic carcinoma (LGACC) is a rare orbital malignancy with devastating lethality. Neoadjuvant intra-arterial chemotherapy (IACC) has demonstrated cytoreductive effects on LGACC macroscopically, but limited studies have examined cellular and molecular determinants of the cytoreductive effect. This post hoc study assessed apoptotic marker expression on excised tumor specimens after neoadjuvant IACC and globe-sparing resection, emphasizing the examination of tumor margins. METHODS: This retrospective study identified LGACC specimens resected in a globe-sparing technique after neoadjuvant IACC by reviewing the Florida Lions Ocular Pathology database at Bascom Palmer Eye Institute. Histopathology slides of the specimens were re-examined to confirm the diagnosis and identify the tumor margin. Immunofluorescent staining was performed for apoptotic markers, including P53, cleaved caspase-3, cleaved PARP-1, and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL). Positive expression was determined by comparison to the negative control. RESULTS: Tumor specimens from 5 patients met inclusion criteria. All 5 cases were positive at the center and the margin for TUNEL, p53, and cleaved caspase-3. One case did not show positive expression of cleaved PARP-1 at the margin but was positive for the other apoptotic markers. CONCLUSIONS: This post hoc study demonstrated positive staining for multiple apoptotic markers in post-IACC tumor specimens at the tumor center and margin. Apoptotic marker expression along the margins of post-treatment specimens is important, as it may offer surrogate information to speculate on the state of residual cancer cells adjacent to the excision margin inadvertently remaining in the orbit.

Time-Resolved Mechanistic Depiction of Photoinduced CO2 Reduction Catalysis on a Urea-Modified Iron Porphyrin.

The development of functional artificial photosynthetic devices relies on the understanding of mechanistic aspects involved in specialized photocatalysts. Modified iron porphyrins have long been explored as efficient catalysts for the light-induced reduction of carbon dioxide (CO2) towards solar fuels. In spite of the advancements in homogeneous catalysis, the development of the next generation of catalysts requires a complete understanding of the fundamental photoinduced processes taking place prior to and after activation of the substrate by the catalyst. In this work, we employ a state-of-the-art nanosecond optical transient absorption spectroscopic setup with a double excitation capability to induce charge accumulation and trigger the reduction of CO2 to carbon monoxide (CO). Our biomimetic system is composed of a urea-modified iron(III) tetraphenylporphyrin (UrFeIII) catalyst, the prototypical [Ru(bpy)3]2+ (bpy=2,2'-bipyridine) used as a photosensitizer, and sodium ascorbate as an electron donor. Under inert atmosphere, we show that two electrons can be successively accumulated on the catalyst as the fates of the photogenerated UrFeII and UrFeI reduced species are tracked. In the presence of CO2, the catalytic cycle is kick-started providing further evidence on CO2 activation by the UrFe catalyst in its formal FeI oxidation state.

CASPT2 study of the electronic structure and photochemistry of protonated N-nitrosodimethylamine (NDMA-H+) at 453 nm.

In this work, we have studied the photodissociation of the protonated derivatives of N-nitrosodimethylamine [(CH3)2N-NO] with the CASPT2 method. It is found that only one of the four possible protonated species of the dialkylnitrosamine compound absorbs in the visible region at 453 nm, that is, N-nitrosoammonium ion [(CH3)2NH-NO]+. This species is also the only one whose first singlet excited state is dissociative to directly yield the aminium radical cation [(CH3)2NHN·]+ and nitric oxide. In addition, we have studied the intramolecular proton migration reaction {[(CH3)2N-NOH]+ → [(CH3)2NH-NO]+} both in the ground and excited state (ESIPT/GSIPT); our results indicate that this process is not accessible neither in the ground nor in the first excited state. Furthermore, as a first approximation, MP2/HF calculations on the nitrosamine-acid complex indicate that in acidic solutions of aprotic solvents, only [(CH3)2NH-NO]+ is formed.

Analytical high-dimensional operators in canonical polyadic finite basis representation (CP-FBR).

In the present work, we introduce a simple means of obtaining an analytical (i.e., grid-free) canonical polyadic (CP) representation of a multidimensional function that is expressed in terms of a set of discrete data. For this, we make use of an initial CP guess, even not fully converged, and a set of auxiliary basis functions [finite basis representation (FBR)]. The resulting CP-FBR expression constitutes the CP counterpart of our previous Tucker sum-of-products-FBR approach. However, as is well-known, CP expressions are much more compact. This has obvious advantages in high-dimensional quantum dynamics. The power of CP-FBR lies in the fact that it requires a grid much coarser than the one needed for the dynamics. In a subsequent step, the basis functions can be interpolated to any desired density of grid points. This is useful, for instance, when different initial conditions (e.g., energy content) of a system are to be considered. We show the application of the method to bound systems of increased dimensionality: H2 (3D), HONO (6D), and CH4 (9D).

Quantum and classical molecular dynamics for H atom scattering from graphene.

This work presents systematic comparisons between classical molecular dynamics (cMD) and quantum dynamics (QD) simulations of 15-dimensional and 75-dimensional models in their description of H atom scattering from graphene. We use an experimentally validated full-dimensional neural network potential energy surface of a hydrogen atom interacting with a large cell of graphene containing 24 carbon atoms. For quantum dynamics simulations, we apply Monte Carlo canonical polyadic decomposition to transform the original potential energy surface (PES) into a sum of products form and use the multi-layer multi-configuration time-dependent Hartree method to simulate the quantum scattering of a hydrogen or deuterium atom with an initial kinetic energy of 1.96 or 0.96 eV and an incident angle of 0°, i.e., perpendicular to the graphene surface. The cMD and QD initial conditions have been carefully chosen in order to be as close as possible. Our results show little differences between cMD and QD simulations when the incident energy of the H atom is equal to 1.96 eV. However, a large difference in sticking probability is observed when the incident energy of the H atom is equal to 0.96 eV, indicating the predominance of quantum effects. To the best of our knowledge, our work provides the first benchmark of quantum against classical simulations for a system of this size with a realistic PES. Additionally, new projectors are implemented in the Heidelberg multi-configuration time-dependent Hartree package for the calculation of the atom scattering energy transfer distribution as a function of outgoing angles.

Nitrene formation is the first step of the thermal and photochemical decomposition reactions of organic azides.

In this work, the decomposition of a prototypical azide, isopropyl azide, both in the ground and excited states, has been investigated through the use of multiconfigurational CASSCF and MS-CASPT2 electronic structure approaches. Particular emphasis has been placed on the thermal reaction starting at the S0 ground state surface. It has been found that the azide thermally decomposes via a stepwise mechanism, whose rate-determining step is the formation of isopropyl nitrene, which is, in turn, the first step of the global mechanism. After that, the nitrene isomerizes to the corresponding imine derivative. Two routes are possible for such a decomposition: (i) a spin-allowed path involving a transition state; and (ii) a spin-forbidden one via a S0/T0 intersystem crossing. Both intermediates have been determined and characterised. Their associated relative energies have been found to be quite similar, 45.75 and 45.52 kcal mol-1, respectively. To complete this study, the kinetics of the singlet and triplet channels are modeled with the MESMER (Master Equation Solver for Multi-Energy Well Reactions) code by applying the RRKM and Landau-Zener (with WKB tunnelling correction) theories, respectively. It is found that the canonical rate-coefficients of the singlet path are 2-orders of magnitude higher than the rate-coefficients of the forbidden reaction. In addition, the concerted mechanism has been investigated that would lead to the formation of the imine derivative and nitrogen extrusion in the first step of the decomposition. After a careful analysis of CASSCF calculations with different active spaces and their comparison with single electronic configuration methods (MP2 and B3LYP), the concerted mechanism is discarded.

Ultrafast CO2 photodissociation in the energy region of the lowest Rydberg series.

We present a detailed theoretical survey of the electronic structure of excited states of the CO2 molecule, with the aim of providing a well-defined theoretical framework for the quantum dynamical studies at energies beyond 12 eV from the ground state. One of the major goals of our work is to emphasize the need for dealing with the presence of both molecular valence and Rydberg states. Although a CASSCF/MRCI approach can be used to appropriately describe the lowest-lying valence states, it becomes incapable of describing the upper electronic states due to the exceedingly large number of electronic excitations required. To circumvent this we employ instead the EOM-CCSD monoconfigurational method to describe the manifold of both valence and Rydberg states in the Franck-Condon region and then a matching procedure to connect these EOM-CCSD eigensolutions with those obtained from CASSCF/MRCI in the outer region, thus ensuring the correct asymptotic behavior. Within this hybrid level of theory, we then analyze the role of valence and Rydberg states in the dynamical mechanism of the photodissociation of quasi-linear CO2 into CO + O fragments, by considering a simple but effective 1D multistate non-adiabatic model for the ultrafast C-O bond break up. We show evidence that the metastability of the Rydberg states must be accounted for in the ultrafast dynamics since they produce changes in the photodissociation yields within the first tens of fs.

Non long-range corrected density functionals incorrectly describe the intensity of the CH stretching band in polycyclic aromatic hydrocarbons.

We present a comprehensive study of the most relevant numerical aspects influencing frequencies and intensities in the infrared spectrum of isolated polycyclic aromatic hydrocarbons (PAHs) regarding the overestimate of the IR CH-stretching bands. We use naphthalene as benchmark and show the validity of our results to different members of the PAH family. Our analysis relies on widely employed density functional theory methods and second-order vibrational perturbational theory for the computation of vibrational eigenstates. We have focused on the elucidation of the origin of the systematic overestimate of the intensities in the CH-stretching region. To rule out nonfundamental numerical errors, we have initially considered the influence of the electronic basis set and various other parameters on the different stages of the vibrational analysis. In a second stage, we have benchmarked the results of different density functional theory functionals with respect to the aforementioned overestimate taken as the ratio between the most prominent features of the spectrum, the CH-bending and the CH-stretching bands. Our results unambiguously indicate that the long-range correction plays a major role in this spurious numerical issue. More specifically, this phenomenon is due to an incorrect description of the charge distribution (and hence dipole) within the symmetrically relevant CH bonds. Long-range correction specifically remedies this issue. It improves the description of the intensities in the stretching region while at the same time it does not perturb significantly the rest of the spectrum. With respect to the frequencies, we have observed an overall improvement when compared to noncorrected functionals.

AutoMeKin2021: An open-source program for automated reaction discovery.

AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922). This release features a number of new capabilities: rare-event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, use of chemical knowledge, a new search algorithm based on bond-order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at: https://rxnkin.usc.es/index.php/AutoMeKin.

A SA-CASSCF and MS-CASPT2 study on the electronic structure of nitrosobenzene and its relation to its dissociation dynamics.

The photodissociation channels of nitrosobenzene (PhNO) induced by a 255 nm photolytic wavelength have been studied using the complete active space self-consistent method and the multistate second-order multiconfigurational perturbation theory. It is found that there exists a triplet route for photodissociation of the molecule. The reaction mechanism consists of a complex cascade of nonadiabatic electronic transitions involving triple and double conical intersections as well as intersystem crossing. Several of the relevant states (S2, S4, and S5 states) correspond to double excitations. It is worth noting that the last step of the photodissociation implies an internal conversion process. The experimentally observed velocity pattern of the NO fragment is a signature of such a conical intersection.

Orbital Hemorrhagic Necrosis, Globe Rupture, and Death From Intraorbital Injection of 1% Sodium Deoxycholate in a Murine Model.

PURPOSE: Deoxycholic acid (DCA) 1% is an injectable detergent indicated for submental fat reduction, although clinically it is being injected off-label for orbital fat prolapse. It is known to cause severe inflammation, local nerve dysfunction, and tissue necrosis, all of which could be catastrophic in the orbit and periocular region. This study evaluated the effects of periocular DCA on orbital and ocular adnexal tissues in a murine model. METHODS: Mice were treated via split-face intraorbital injections, subcutaneous injections, and topical cornea application with DCA versus phosphate-buffered saline. Whole heads were fixed, decalcified, and sectioned for orbital histology after 1-7 days. Matched pairs of human globes and mouse globes were immersed in either phosphate-buffered saline or 1% DCA for 72 hours. RESULTS: Six of 11 mice receiving intraorbital DCA injections died within minutes. Surviving mice developed severe orbital inflammatory necrosis. All orbits injected with phosphate-buffered saline were clinically and histologically normal. Six mice were treated with lower concentrations of DCA and all developed variable amounts of orbital inflammation, hemorrhage, and globe necrosis. Mice receiving subcutaneous DCA injection to the lower eyelid showed inflammatory necrosis, edema, and lid malposition. Topical application of DCA to mouse corneas caused no external or histologic changes. Human and mouse globes immersed ex vivo in DCA developed corneal edema and cataract formation without observable scleral changes. CONCLUSION: Intraorbital and periocular injection of DCA can cause devastating complications in a murine model, and significant caution is advised for off-label use in the periocular region.

Mitochondrial targeted therapy with elamipretide (MTP-131) as an adjunct to tumor necrosis factor inhibition for traumatic optic neuropathy in the acute setting.

Traumatic optic neuropathy (TON) can occur following blunt trauma to the orbit and can lead to permanent vision loss. In this study, we investigated the effectiveness of elamipretide (MTP-131), a small mitochondrially-targeted tetrapeptide, in conjunction with etanercept, a tumor necrosis factor (TNF) inhibitor, as neuroprotective agents of retinal ganglion cells (RGCs) after optic nerve trauma with sonication-induced TON (SI-TON) in mice. Treatment with intravitreal MTP-131 and subcutaneous etanercept and MTP-131 showed a 21% increase (p < 0.01) in RGC survival rate compared to PBS-treated control eyes. Subcutaneous etanercept and MTP-131 had an 11% increase (p < 0.05) in RGC survival compared to controls. Subcutaneous etanercept only group showed 20% increase (p < 0.01) in RGC survival compared to controls, while subcutaneous MTP-131 alone showed a 17% increase (p < 0.01). Surprisingly, we did not observe a synergistic effect between the two drugs in the group receiving both etanercept and MTP-131. One possible explanation for the absence of a synergistic effect is that MTP-131 and etanercept may be acting on different portions of the same pathway.

Low-rank sum-of-products finite-basis-representation (SOP-FBR) of potential energy surfaces.

The sum-of-products finite-basis-representation (SOP-FBR) approach for the automated multidimensional fit of potential energy surfaces (PESs) is presented. In its current implementation, the method yields a PES in the so-called Tucker sum-of-products form, but it is not restricted to this specific ansatz. The novelty of our algorithm lies in the fact that the fit is performed in terms of a direct product of a Schmidt basis, also known as natural potentials. These encode in a non-trivial way all the physics of the problem and, hence, circumvent the usual extra ad hoc and a posteriori adjustments (e.g., damping functions) of the fitted PES. Moreover, we avoid the intermediate refitting stage common to other tensor-decomposition methods, typically used in the context of nuclear quantum dynamics. The resulting SOP-FBR PES is analytical and differentiable ad infinitum. Our ansatz is fully general and can be used in combination with most (molecular) dynamics codes. In particular, it has been interfaced and extensively tested with the Heidelberg implementation of the multiconfiguration time-dependent Hartree quantum dynamical software package.

Cellular and molecular assessment of rose bengal photodynamic antimicrobial therapy on keratocytes, corneal endothelium and limbal stem cell niche.

Rose Bengal Photodynamic Antimicrobial Therapy (RB-PDAT) is a novel potential treatment for progressive infectious keratitis. The principle behind this therapy is using Rose Bengal as a photosensitizer that can be activated by green light and results in the production of oxygen free radicals which in turn eradicate the microorganism. Given RB-PDAT's mechanism of action and the potential cytotoxic effects, concerns regarding the safety of this technique have arisen. The purpose of this study was to evaluate the effect of RB-PDAT on keratocytes, while focusing on the safety profile that the photo-chemical reaction has on the limbal stem cell (LSC) niche and endothelial cell layer of the treated cornea. To perform RB-PDAT, Rose Bengal solution (0.1% RB in BSS) was applied to the right cornea of rabbits for 30 min and then irradiated by a custom-made green LED light source (525 nm, 6 mW/cm2) for 15 min (5.4 J/cm2). Three rabbits were sacrificed and enucleated after 24 h for evaluation. TUNEL assay and immunohistochemistry for endothelium and limbal stem cell viability were performed on whole mounts and frozen sections in treated and control eyes. LSC of both eyes were isolated and cultured to perform MTT viability and proliferation, and scratch wound healing assays under time-lapse microscopy. Interestingly, while Rose Bengal dye penetration was superficial, yet associated cellular apoptosis was evidenced in up to 1/3 of the stromal thickness on frozen sections. TUNEL assay on whole mounts showed no endothelial cell death following treatment. Immunohistochemistry on frozen sections of LSC displayed no structural difference between treated and non-treated eyes. There was no difference in LSC proliferation rates and scratch wound healing assay demonstrated adequate cell migration from treated and non-treated eyes. The current study suggests that even though penetration of the RB dye has been shown to be limited, oxidative stress produced by RB-PDAT can reach deeper into the corneal stroma. Nevertheless, our results show that performing RB-PDAT is safe on the corneal endothelium and has no effect on LSC viability or function.

Conical intersections and intersystem crossings explain product formation in photochemical reactions of aryl azides.

Photochemistry of 3- and 4-methoxyphenyl azide at 266 nm has been studied by means of the complete active space self-consistent field (CASSCF) and multi-configurational second-order perturbation (MS-CASPT2) methods. Minima and interstate crossing points have been optimized using the CASSCF method. The calculations predict that the key step of the photolysis of both azides is a non-radiative process. However, an important difference is found when we compare the reactivity of both isomers of azide, deactivation of 3-methoxyphenyl azide (1) can occur via two reaction channels (internal conversion or intersystem crossing), which lead to formation of the dimer of 2H-azepine derivative (2a) and 3,3'-dimethoxyazobenzene (2b). In contrast, deactivation of 4-methoxyphenyl azide (3) takes place via a singlet to triplet intersystem crossing, which leads to formation of 4,4'-dimethoxyazobenzene (4). After initial deactivation, both isomers follow a cascade of surface crossings until they reach the final nitrenes, respectively. The reference active space for the two azides is 14 electrons in 13 orbitals and comprises the six π-type orbitals of the aromatic ring plus four σ-(N-N2) and five π-type orbitals of the -N3 moiety.

Therapeutic targeting of oncogenic transcription factors by natural products in eye cancer.

Carcinogenesis has a multifactorial etiology, and the underlying molecular pathogenesis is still not entirely understood, especially for eye cancers. Primary malignant intraocular neoplasms are relatively rare, but delayed detection and inappropriate management contribute to poor outcomes. Conventional treatment, such as orbital exenteration, chemotherapy, or radiotherapy, alone results in high mortality for many of these malignancies. Recent sequential multimodal therapy with a combination of high-dose chemotherapy, followed by appropriate surgery, radiotherapy, and additional adjuvant chemotherapy has helped dramatically improve management. Transcription factors are proteins that regulate gene expression by modulating the synthesis of mRNA. Since transcription is a dominant control point in the production of many proteins, transcription factors represent key regulators for numerous cellular functions, including proliferation, differentiation, and apoptosis, making them compelling targets for drug development. Natural compounds have been studied for their potential to be potent yet safe chemotherapeutic drugs. Since the ancient times, plant-derived bioactive molecules have been used to treat dreadful diseases like cancer, and several refined pharmaceutics have been developed from these compounds. Understanding targeting mechanisms of oncogenic transcription factors by natural products can add to our oncologic management toolbox. This review summarizes the current findings of natural products in targeting specific oncogenic transcription factors in various types of eye cancer.

Entangled Photonic-Nuclear Molecular Dynamics of LiF in Quantum Optical Cavities.

The quantum photodynamics of a simple diatomic molecule with a permanent dipole immersed within an optical cavity containing a quantized radiation field is studied in detail. The chosen molecule under study, lithium fluoride (LiF), is characterized by the presence of an avoided crossing between the two lowest 1Σ potential energy curves (covalent-ionic diabatic crossing). Without field, after prompt excitation from the ground state 1 1Σ, the excited nuclear wave packet moves back and forth in the upper 2 1Σ state, but in the proximity of the avoided crossing, the nonadiabatic coupling transfers part of the nuclear wave packet to the lower 1 1Σ state, which eventually leads to dissociation. The quantized field of a cavity also induces an additional light crossing in the modified dressed potential energy curves with similar transfer properties. To understand the entangled photonic-nuclear dynamics, we solve the time-dependent Schrödinger equation by using the multiconfigurational time-dependent Hartree method (MCTDH). The single mode quantized field of the cavity is represented in the coordinate space instead of in the Fock space, which allows us to deal with the field as an additional vibrational mode within the MCTDH procedure on equal footing. We prepare the cavity with different quantum states of light, namely, Fock states, coherent states, and squeezed coherent states. Our results reveal pure quantum light effects on the molecular photodynamics and the dissociation yields of LiF, which are quite different from the light-undressed case and which cannot be described in general by a semiclassical approach using classical electromagnetic fields.